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- EMDB-18657: PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cull... -

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Basic information

Entry
Database: EMDB / ID: EMD-18657
TitlePROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1
Map datasharpened by deepemhancer
Sample
  • Complex: KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1
    • Protein or peptide: von Hippel-Lindau disease tumor suppressor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-2
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: GTPase KRas
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide
KeywordsTARGETED PROTEIN DEGRADATION / PROTAC / GTPASE / TRANSFERASE
Function / homology
Function and homology information


regulation of cellular response to hypoxia / negative regulation of beige fat cell differentiation / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling ...regulation of cellular response to hypoxia / negative regulation of beige fat cell differentiation / negative regulation of receptor signaling pathway via JAK-STAT / RHOBTB3 ATPase cycle / cullin-RING-type E3 NEDD8 transferase / NEDD8 transferase activity / cullin-RING ubiquitin ligase complex / Cul7-RING ubiquitin ligase complex / cellular response to chemical stress / Loss of Function of FBXW7 in Cancer and NOTCH1 Signaling / target-directed miRNA degradation / elongin complex / positive regulation of protein autoubiquitination / RNA polymerase II transcription initiation surveillance / protein neddylation / Replication of the SARS-CoV-1 genome / transcription elongation factor activity / NEDD8 ligase activity / protein K27-linked ubiquitination / negative regulation of response to oxidative stress / VCB complex / Cul5-RING ubiquitin ligase complex / ubiquitin-ubiquitin ligase activity / response to mineralocorticoid / GMP binding / ubiquitin-dependent protein catabolic process via the C-end degron rule pathway / SCF ubiquitin ligase complex / forebrain astrocyte development / Cul2-RING ubiquitin ligase complex / LRR domain binding / SUMOylation of ubiquitinylation proteins / Cul3-RING ubiquitin ligase complex / negative regulation of type I interferon production / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / Cul4A-RING E3 ubiquitin ligase complex / Prolactin receptor signaling / Cul4-RING E3 ubiquitin ligase complex / negative regulation of mitophagy / response to gravity / epithelial tube branching involved in lung morphogenesis / Cul4B-RING E3 ubiquitin ligase complex / type I pneumocyte differentiation / ubiquitin ligase complex scaffold activity / Rac protein signal transduction / negative regulation of transcription elongation by RNA polymerase II / myoblast proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Pausing and recovery of Tat-mediated HIV elongation / Tat-mediated HIV elongation arrest and recovery / Activation of RAS in B cells / HIV elongation arrest and recovery / Pausing and recovery of HIV elongation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / skeletal muscle cell differentiation / cullin family protein binding / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / cardiac muscle cell proliferation / SHC1 events in ERBB4 signaling / negative regulation of signal transduction / Signalling to RAS / protein monoubiquitination / Tat-mediated elongation of the HIV-1 transcript / Formation of HIV-1 elongation complex containing HIV-1 Tat / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / Formation of HIV elongation complex in the absence of HIV Tat / glial cell proliferation / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / ubiquitin-like ligase-substrate adaptor activity / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / site of DNA damage / RNA Polymerase II Transcription Elongation / Signaling by FGFR4 in disease / Signaling by CSF3 (G-CSF) / Formation of RNA Pol II elongation complex / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / signal transduction in response to DNA damage / p38MAPK events / Signaling by FGFR3 in disease / striated muscle cell differentiation
Similarity search - Function
von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain ...von Hippel-Lindau disease tumour suppressor, beta/alpha domain / von Hippel-Lindau disease tumour suppressor, alpha domain / von Hippel-Lindau disease tumour suppressor, beta domain / VHL superfamily / von Hippel-Lindau disease tumour suppressor, alpha domain superfamily / von Hippel-Lindau disease tumour suppressor, beta domain superfamily / VHL beta domain / VHL box domain / Zinc finger, RING-H2-type / RING-H2 zinc finger domain / Cullin, N-terminal / Cullin protein neddylation domain / : / Cullin, conserved site / Cullin alpha solenoid domain / Cullin family signature. / Elongin-C / Elongin B / Cullin repeat-like-containing domain superfamily / Cullin protein, neddylation domain / Cullin / Cullin protein neddylation domain / Cullin / : / Cullin alpha+beta domain / Cullin homology domain / Cullin homology domain superfamily / Cullin family profile. / S-phase kinase-associated protein 1-like / SKP1 component, POZ domain / Skp1 family, tetramerisation domain / Found in Skp1 protein family / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / SKP1/BTB/POZ domain superfamily / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Zinc finger RING-type profile. / Zinc finger, RING-type / Small GTP-binding protein domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GTPase KRas / von Hippel-Lindau disease tumor suppressor / E3 ubiquitin-protein ligase RBX1 / Cullin-2 / Elongin-C / Elongin-B
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsFischer G / Peter D / Arce-Solano S
Funding support Austria, 1 items
OrganizationGrant numberCountry
Other privateBoehringer Ingelheim Austria
Citation
Journal: Science / Year: 2024
Title: Targeting cancer with small-molecule pan-KRAS degraders.
Authors: Johannes Popow / William Farnaby / Andreas Gollner / Christiane Kofink / Gerhard Fischer / Melanie Wurm / David Zollman / Andre Wijaya / Nikolai Mischerikow / Carina Hasenoehrl / Polina ...Authors: Johannes Popow / William Farnaby / Andreas Gollner / Christiane Kofink / Gerhard Fischer / Melanie Wurm / David Zollman / Andre Wijaya / Nikolai Mischerikow / Carina Hasenoehrl / Polina Prokofeva / Heribert Arnhof / Silvia Arce-Solano / Sammy Bell / Georg Boeck / Emelyne Diers / Aileen B Frost / Jake Goodwin-Tindall / Jale Karolyi-Oezguer / Shakil Khan / Theresa Klawatsch / Manfred Koegl / Roland Kousek / Barbara Kratochvil / Katrin Kropatsch / Arnel A Lauber / Ross McLennan / Sabine Olt / Daniel Peter / Oliver Petermann / Vanessa Roessler / Peggy Stolt-Bergner / Patrick Strack / Eva Strauss / Nicole Trainor / Vesna Vetma / Claire Whitworth / Siying Zhong / Jens Quant / Harald Weinstabl / Bernhard Kuster / Peter Ettmayer / Alessio Ciulli /
Abstract: Mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) protein are highly prevalent in cancer. However, small-molecule concepts that address oncogenic KRAS alleles remain elusive beyond ...Mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) protein are highly prevalent in cancer. However, small-molecule concepts that address oncogenic KRAS alleles remain elusive beyond replacing glycine at position 12 with cysteine (G12C), which is clinically drugged through covalent inhibitors. Guided by biophysical and structural studies of ternary complexes, we designed a heterobifunctional small molecule that potently degrades 13 out of 17 of the most prevalent oncogenic KRAS alleles. Compared with inhibition, KRAS degradation results in more profound and sustained pathway modulation across a broad range of KRAS mutant cell lines, killing cancer cells while sparing models without genetic KRAS aberrations. Pharmacological degradation of oncogenic KRAS was tolerated and led to tumor regression in vivo. Together, these findings unveil a new path toward addressing KRAS-driven cancers with small-molecule degraders.
#1: Journal: Biorxiv / Year: 2023
Title: Targeting cancer with small molecule pan-KRAS degraders
Authors: Popow J / Farnaby W / Gollner A / Kofink C / Fischer G / Wurm M / Zollman D / Wijaya A / Mischerikow N / Hasenoehrl C / Prokofeva P / Arnhof H / Arce-Solano S / Bell S / Boeck G / Diers E / ...Authors: Popow J / Farnaby W / Gollner A / Kofink C / Fischer G / Wurm M / Zollman D / Wijaya A / Mischerikow N / Hasenoehrl C / Prokofeva P / Arnhof H / Arce-Solano S / Bell S / Boeck G / Diers E / Frost A / Goodwin-Tindall J / Karolyi-Oezguer J / Khan S / Klawatsch T / Koegl M / Kousek R / Kratochvil B / Kropatsch K / Lauber A / McLennan R / Olt S / Peter D / Petermann O / Roessler V / Stolt-Bergner P / Strack P / Strauss E / Trainor N / Vetma V / Whitworth C / Zhong S / Quant J / Weinstabl H / Kuster B / Ettmayer P / Ciulli A
History
DepositionOct 14, 2023-
Header (metadata) releaseDec 6, 2023-
Map releaseDec 6, 2023-
UpdateOct 2, 2024-
Current statusOct 2, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18657.png

Downloads & links

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Map

FileDownload / File: emd_18657.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened by deepemhancer
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 384 pix.
= 381.44 Å		0.99 Å/pix.
x 384 pix.
= 381.44 Å		0.99 Å/pix.
x 384 pix.
= 381.44 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-0.000902001 - 2.3546982
Average (Standard dev.)0.0013088719 (±0.0283065)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 381.44 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: unsharpened map from 3D flex

Fileemd_18657_additional_1.map
Annotationunsharpened map from 3D flex
Projections & Slices
AxesZYX

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Half map: half map B

Fileemd_18657_half_map_1.map
Annotationhalf map B
Projections & Slices
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Half map: half map A

Fileemd_18657_half_map_2.map
Annotationhalf map A
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Sample components

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Entire : KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1

EntireName: KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1
Components
  • Complex: KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1
    • Protein or peptide: von Hippel-Lindau disease tumor suppressor
    • Protein or peptide: Elongin-B
    • Protein or peptide: Elongin-C
    • Protein or peptide: Cullin-2
    • Protein or peptide: E3 ubiquitin-protein ligase RBX1, N-terminally processed
    • Protein or peptide: GTPase KRas
  • Ligand: ZINC ION
  • Ligand: GUANOSINE-5'-DIPHOSPHATE
  • Ligand: (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide

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Supramolecule #1: KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1

SupramoleculeName: KRAS/ACBI3/VHL/EloB/EloC/Cul2/Rbx1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Details: PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 168 KDa

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Macromolecule #1: von Hippel-Lindau disease tumor suppressor

MacromoleculeName: von Hippel-Lindau disease tumor suppressor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.049545 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: PRRAENWDEA EVGAEEAGVE EYGPEEDGGE ESGAEESGPE ESGPEELGAE EEMEAGRPRP VLRSVNSREP SQVIFCNRSP RVVLPVWLN FDGEPQPYPT LPPGTGRRIH SYRGHLWLFR DAGTHDGLLV NQTELFVPSL NVDGQPIFAN ITLPVYTLKE R CLQVVRSL ...String:
PRRAENWDEA EVGAEEAGVE EYGPEEDGGE ESGAEESGPE ESGPEELGAE EEMEAGRPRP VLRSVNSREP SQVIFCNRSP RVVLPVWLN FDGEPQPYPT LPPGTGRRIH SYRGHLWLFR DAGTHDGLLV NQTELFVPSL NVDGQPIFAN ITLPVYTLKE R CLQVVRSL VKPENYRRLD IVRSLYEDLE DHPNVQKDLE RLTQERIAHQ RMGD

UniProtKB: von Hippel-Lindau disease tumor suppressor

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Macromolecule #2: Elongin-B

MacromoleculeName: Elongin-B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.016586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DVFLMIRRHK TTIFTDAKES STVFELKRIV EGILKRPPDE QRLYKDDQLL DDGKTLGECG FTSQTARPQA PATVGLAFRA DDTFEALCI EPFSSPPELP DVMKPQDSGS SANEQAVQ

UniProtKB: Elongin-B

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Macromolecule #3: Elongin-C

MacromoleculeName: Elongin-C / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.353939 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DGEEKTYGGC EGPDAMYVKL ISSDGHEFIV KREHALTSGT IKAMLSGPGQ FAENETNEVN FREIPSHVLS KVCMYFTYKV RYTNSSTEI PEFPIAPEIA LELLMAANFL DC

UniProtKB: Elongin-C

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Macromolecule #4: Cullin-2

MacromoleculeName: Cullin-2 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.967734 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SLKPRVVDFD ETWNKLLTTI KAVVMLEYVE RATWNDRFSD IYALCVAYPE PLGERLYTET KIFLENHVRH LHKRVLESEE QVLVMYHRY WEEYSKGADY MDCLYRYLNT QFIKKNKLTE ADLQYGYGGV DMNEPLMEIG ELALDMWRKL MVEPLQAILI R MLLREIKN ...String:
SLKPRVVDFD ETWNKLLTTI KAVVMLEYVE RATWNDRFSD IYALCVAYPE PLGERLYTET KIFLENHVRH LHKRVLESEE QVLVMYHRY WEEYSKGADY MDCLYRYLNT QFIKKNKLTE ADLQYGYGGV DMNEPLMEIG ELALDMWRKL MVEPLQAILI R MLLREIKN DRGGEDPNQK VIHGVINSFV HVEQYKKKFP LKFYQEIFES PFLTETGEYY KQEASNLLQE SNCSQYMEKV LG RLKDEEI RCRKYLHPSS YTKVIHECQQ RMVADHLQFL HAECHNIIRQ EKKNDMANMY VLLRAVSTGL PHMIQELQNH IHD EGLRAT SNLTQENMPT LFVESVLEVH GKFVQLINTV LNGDQHFMSA LDKALTSVVN YREPKSVCKA PELLAKYCDN LLKK SAKGM TENEVEDRLT SFITVFKYID DKDVFQKFYA RMLAKRLIHG LSMSMDSEEA MINKLKQACG YEFTSKLHRM YTDMS VSAD LNNKFNNFIK NQDTVIDLGI SFQIYVLQAG AWPLTQAPSS TFAIPQELEK SVQMFELFYS QHFSGRKLTW LHYLCT GEV KMNYLGKPYV AMVTTYQMAV LLAFNNSETV SYKELQDSTQ MNEKELTKTI KSLLDVKMIN HDSEKEDIDA ESSFSLN MN FSSKRTKFKI TTSMQKDTPQ EMEQTRSAVD EDRKMYLQAA IVRIMKARKV LRHNALIQEV ISQSRARFNP SISMIKKC I EVLIDKQYIE RSQASADEYS YVA

UniProtKB: Cullin-2

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Macromolecule #5: E3 ubiquitin-protein ligase RBX1, N-terminally processed

MacromoleculeName: E3 ubiquitin-protein ligase RBX1, N-terminally processed
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.15878 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AAAMDVDTPS GTNSGAGKKR FEVKKWNAVA LWAWDIVVDN CAICRNHIMD LCIECQANQA SATSEECTVA WGVCNHAFHF HCISRWLKT RQVCPLDNRE WEFQKYGH

UniProtKB: E3 ubiquitin-protein ligase RBX1

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Macromolecule #6: GTPase KRas

MacromoleculeName: GTPase KRas / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 19.354824 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GMTEYKLVVV GAVGVGKSAL TIQLIQNHFV DEYDPTIEDS YRKQVVIDGE TCLLDILDTA GQEEYSAMRD QYMRTGEGFL CVFAINNTK SFEDIHHYRE QIKRVKDSED VPMVLVGNKS DLPSRTVDTK QAQDLARSYG IPFIETSAKT RQGVDDAFYT L VREIRKHK EK

UniProtKB: GTPase KRas

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Macromolecule #7: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 7 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #8: GUANOSINE-5'-DIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-DIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: GDP
Molecular weightTheoretical: 443.201 Da
Chemical component information

ChemComp-GDP:
GUANOSINE-5'-DIPHOSPHATE / GDP, energy-carrying molecule*YM

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Macromolecule #9: (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-me...

MacromoleculeName: (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol- ...Name: (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide
type: ligand / ID: 9 / Number of copies: 1 / Formula: WYL
Molecular weightTheoretical: 1.019247 KDa
Chemical component information

ChemComp-WYL:
(2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.916 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormula
50.0 mMTRIS
100.0 mMNaCl
0.5 mMTCEP
2.0 mMMgCl2
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 4 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 7634 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2414442 / Details: before 2D classification
Startup modelType of model: NONE / Details: cryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: cryoSPARC (ver. 4) / Software - details: 3Dflex reconstruction / Details: cryoSPARC 3Dflex reconstruction / Number images used: 217000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3)
Final 3D classificationNumber classes: 3 / Avg.num./class: 162900 / Software - Name: cryoSPARC (ver. 3)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5n4w


Chain - Chain ID: F / Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: KRAS-structure
Output model

PDB-8qu8:
PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1

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